I have an install set up with ALL my mods installed, and a number of parts still need to be updated, I have a patch which assigns a nonexistent size to all parts which are missing the bulkheadProfiles line.
In the editor, went into to the filter-by-size, and while those parts didn't show up there, and there wasn't any extra icons, nothing funny happened

Well, I just finished with all my mods, as far as I can tell.
Next up is for me to create a test install, load ALL my mods, and have a catchall like this:
@PART[*]:HAS[~bulkheadProfiles[]]
{
bulkheadProfiles = missingSrf
}
Then, I'll start the game, get to the main menu and exit. After this, all I'll need to do is search the ModuleManager.ConfigCache for any missingSrf which will point me to any I missed.
Since you are go through many other mods, you might want to do the same. I did find that while your find/greps were good, they came up with a few false positives, and I may have missed some.

STS-4/4R completed, in a two-part mission.
STS-4 was last week, and appropriately enough, suffered a mishap during the launch (fairing took out the vertical tail fin), so it was unable to return. I used the engines to maneuver into a high orbit (>350 km), inclined at slightly less thank 20 degrees (19.570). I was then haunted by the extremely bad placement and balancing of the RCS thrusters on the rescue vessel, to the point that I stopped and continued last night (a week later).
STS-4R went off last night, after rebalancing the RCS on the shuttle. The shuttles have an extendable docking port in the bay, and my intention was to dock them together. If I had only wanted to do an EVA rescue, I could have done that last week (actually started to do that, but stopped for various reasons)
STS-4R got off to a rocky start, some game issues forced a restart, as well as my fat fingers messing up on the keyboard. But the final mission wasn't too bad, although the docking isn't anything to write home about, it did work.
My reentry and landings are getting better. I only needed the engines because I misjudged my altitude and needed a boost of speed for about 10 seconds just before landing (so I wouldn't stall out).
One minor quibble with the rules.
On to the show.
Complete video of both missions here:
STS-4 Launch
The accident:
The rescue mission, STS-4R
Orbital Maneuvers
The two docked shuttles
Reentry & landing
Post-mission Portraits